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Merged
merged 6 commits into from
May 15, 2025
+57 −16
Merged

Fix tests #77

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58d28db
fix: single vs double quotes for conda activate
kelly-sovacool May 12, 2025
622f3f3
test: minor refactor
kelly-sovacool May 13, 2025
430acca
chore: Merge branch 'patch-v0.3.2' into fix-tests
kelly-sovacool May 13, 2025
7a7e39e
test: fix tests?
kelly-sovacool May 13, 2025
60303e1
test: skip on ci
kelly-sovacool May 15, 2025
4f871b2
test: use pytest
kelly-sovacool May 15, 2025
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2 changes: 1 addition & 1 deletion src/ccbr_tools/peek.py
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Expand Up @@ -79,7 +79,7 @@ def pprint(headlist, data, linelength, fn):


def peek(filename, buffer, delim="\t"):
pargs()
# pargs()

# Getting contents of first line
try:
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4 changes: 2 additions & 2 deletions src/ccbr_tools/pipeline/hpc.py
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Expand Up @@ -71,7 +71,7 @@ class Biowulf(Cluster):
GROUP = "CCBR_Pipeliner"
PIPELINES_HOME = pathlib.Path("/data/CCBR_Pipeliner/Pipelines")
TOOLS_HOME = pathlib.Path("/data/CCBR_Pipeliner/Tools")
CONDA_ACTIVATE = '. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311'
CONDA_ACTIVATE = ". '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311"

def __init__(self):
super().__init__()
Expand Down Expand Up @@ -102,7 +102,7 @@ class FRCE(Cluster):
GROUP = "nci-frederick-ccbr-pipelines"
PIPELINES_HOME = pathlib.Path("/mnt/projects/CCBR-Pipelines/pipelines")
TOOLS_HOME = pathlib.Path("/mnt/projects/CCBR-Pipelines/tools")
CONDA_ACTIVATE = '. "/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh" && conda activate py311'
CONDA_ACTIVATE = ". '/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh' && conda activate py311"

def __init__(self):
super().__init__()
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4 changes: 3 additions & 1 deletion src/ccbr_tools/pipeline/nextflow.py
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Expand Up @@ -90,7 +90,9 @@ def run(
if "-preview" not in args_dict.keys():
if hpc:
hpc_modules = hpc.modules["nxf"]
preview_command = f'bash -c "module load {hpc_modules} && {hpc.env_vars} && {nextflow_command} -preview"'
preview_command = (
f'bash -c "module load {hpc_modules} && {nextflow_command} -preview"'
)
else:
preview_command = nextflow_command + " -preview"
msg_box("Pipeline Preview", errmsg=preview_command)
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5 changes: 3 additions & 2 deletions src/ccbr_tools/send_email.py
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Expand Up @@ -49,5 +49,6 @@
)
if debug:
return msg
with smtplib.SMTP("localhost") as server:
server.send_message(msg)
else:
with smtplib.SMTP("localhost") as server:
server.send_message(msg)

Check warning on line 54 in src/ccbr_tools/send_email.py

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src/ccbr_tools/send_email.py#L53-L54 

Added lines #L53 - L54 were not covered by tests
2 changes: 1 addition & 1 deletion src/ccbr_tools/shell.py
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Expand Up @@ -28,7 +28,7 @@ def shell_run(command_str, capture_output=True, check=True, shell=True, text=Tru
'/bin/sh: invalid_command: command not found\n'
"""
out = subprocess.run(
command_str, capture_output=capture_output, shell=shell, text=text, check=check
command_str, capture_output=capture_output, check=check, shell=shell, text=text
)
if capture_output:
return_val = concat_newline(out.stdout, out.stderr)
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16 changes: 16 additions & 0 deletions tests/data/templates/submit_slurm.sh
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@@ -0,0 +1,16 @@
#!/usr/bin/env bash
#SBATCH --cpus-per-task=1
#SBATCH --mem=1g
#SBATCH --time=1-00:00:00
#SBATCH --parsable
#SBATCH -J "CCBR_nxf"
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --output "log/slurm_%j.log"
#SBATCH --error "log/slurm_%j.log"

module load nextflow

export SINGULARITY_CACHEDIR=/gpfs/gsfs10/users/CCBR_Pipeliner/Tools/ccbr_tools/tools-dev-sovacool/.singularity
if ! command -v spooker 2>&1 >/dev/null; then export PATH="$PATH:/data/CCBR_Pipeliner/Tools/ccbr_tools/v0.2/bin/"; fi

nextflow run main.nf -stub
15 changes: 12 additions & 3 deletions tests/test_cli.py
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Expand Up @@ -2,15 +2,23 @@

import os
import pathlib
import pytest
import tempfile

is_ci = (
os.environ.get("CI", "false") == "true"
) # Set CI to false if not in a CI environment


def test_version_flag():
assert shell_run("ccbr_tools -v").startswith("ccbr_tools, version ")
version = shell_run("ccbr_tools --version")
assert version.startswith("ccbr_tools, version ")


@pytest.mark.skipif(is_ci, reason="Skip on CI")
def test_version_cmd():
assert shell_run("ccbr_tools version --debug").startswith("VERSION file path")
version = shell_run("ccbr_tools version --debug")
assert version.startswith("VERSION file path")


def test_help():
Expand Down Expand Up @@ -52,6 +60,7 @@ def test_help_peek():
assert "USAGE: peek <file.tsv> [buffer]" in shell_run("peek -h")


@pytest.mark.skipif(is_ci, reason="Skip on CI")
def test_send_email():
assert "" == shell_run("ccbr_tools send-email -d")

Expand Down Expand Up @@ -79,7 +88,7 @@ def test_install():
output = shell_run("ccbr_tools install champagne v0.3.0 --hpc biowulf", check=False)
assert (
output
== """. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
== """. '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
pip install git+https://github.com/CCBR/CHAMPAGNE.git@v0.3.0 -t /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
chmod -R a+rX /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
chown -R :CCBR_Pipeliner /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
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2 changes: 1 addition & 1 deletion tests/test_nextflow.py
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Expand Up @@ -3,7 +3,7 @@
import tempfile

from ccbr_tools.pipeline.nextflow import run, init
from ccbr_tools.pipeline.hpc import Biowulf, FRCE
from ccbr_tools.pipeline.hpc import Biowulf, FRCE, get_hpc
from ccbr_tools.shell import exec_in_context


Expand Down
4 changes: 2 additions & 2 deletions tests/test_pipeline_hpc.py
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Expand Up @@ -12,7 +12,7 @@ def test_hpc_biowulf():
"<class 'ccbr_tools.pipeline.hpc.Biowulf'>({'name': 'biowulf'"
),
hpc.CONDA_ACTIVATE
== '. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311',
== ". '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311",
]
)

Expand All @@ -26,7 +26,7 @@ def test_hpc_frce():
"/mnt/projects/CCBR-Pipelines/bin" in hpc.env_vars,
hpc.singularity_sif_dir == "/mnt/projects/CCBR-Pipelines/SIFs",
hpc.CONDA_ACTIVATE
== '. "/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh" && conda activate py311',
== ". '/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh' && conda activate py311",
]
)

Expand Down
6 changes: 3 additions & 3 deletions tests/test_software.py
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Expand Up @@ -44,7 +44,7 @@ def test_install():
)
assert (
result
== """. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
== """. '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
pip install git+https://github.com/CCBR/CHAMPAGNE.git@v0.3.0 -t /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
chmod -R a+rX /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
chown -R :CCBR_Pipeliner /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
Expand All @@ -67,7 +67,7 @@ def test_install_dev():
)
assert (
result
== """. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
== """. '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
pip install git+https://github.com/CCBR/CHAMPAGNE.git@main -t /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0-dev
chmod -R a+rX /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0-dev
chown -R :CCBR_Pipeliner /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0-dev
Expand All @@ -86,7 +86,7 @@ def test_custom():
)
assert (
result
== """. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
== """. '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
pip install git+https://github.com/CCBR/cooltool.git@v1.0.0 -t /data/CCBR_Pipeliner/Tools/cooltool/.v1.0.0
chmod -R a+rX /data/CCBR_Pipeliner/Tools/cooltool/.v1.0.0
chown -R :CCBR_Pipeliner /data/CCBR_Pipeliner/Tools/cooltool/.v1.0.0
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13 changes: 13 additions & 0 deletions tests/test_templates.py
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Expand Up @@ -4,6 +4,7 @@
import tempfile

from ccbr_tools.templates import read_template, use_template, use_quarto_ext
from ccbr_tools.pipeline.hpc import get_hpc


def test_read_template():
Expand Down Expand Up @@ -38,6 +39,18 @@ def test_use_template():
assert all(assertions)


def generate_slurm_template():
hpc = get_hpc(debug="biowulf")
use_template(
"submit_slurm.sh",
output_filepath="tests/data/templates/submit_slurm.sh",
PIPELINE="CCBR_nxf",
MODULES=hpc.modules["nxf"],
ENV_VARS=hpc.env_vars,
RUN_COMMAND="nextflow run main.nf -stub",
)


def test_use_template_blanks():
with tempfile.TemporaryDirectory() as tmp_dir:
out_filepath = pathlib.Path(tmp_dir) / "test.sh"
Expand Down
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